Project Summary Differential Proteomics, Inc., is developing a new proteomics technology for comparing the protein composition of biological samples. The technology, Differential Capture Proteomics (DCP), is designed to circumvent serious limitations in the current capabilities of current proteomics technology, notably DCP can identify the protein differences between two body fluid or tissue samples and simultaneously generate an affinity reagent for each identified difference protein. The DCP approach utilizes phage display libraries of peptides from which affinity reagents against the protein components of two samples are isolated. A novel subtraction step removes those affinity reagents against proteins held in common between the two samples, leaving affinity reagents against the difference proteins. These affinity reagents are used to purify the difference proteins, which are then identified using mass spectrometry. DCP will provide a fast, cost-effective process for performing differential proteomic analyses. It will accelerate the pace of biomarker discovery and also simultaneously provide affinity reagents for those biomarkers. These affinity reagents will immediately be available for the development of diagnostic tests for the biomarkers. Thus DCP will play an important role in medicine and biomedical research wherever biomarkers are involved, including disease diagnosis, the monitoring of disease progression, drug discovery and development and the monitoring of drug efficacy in patients. Phase I of this project will build on the success of preliminary experiments and will determine conditions for performing the initial, phage display steps of the DCP process. The format of column chromatography will be used in place of the batch selection protocols currently used for phage display selections. Phase I has 4 specific aims, each of which will optimize a particular step in the phage display portion of the DCP process. Together, specific Aims 1 and 2 will determine the optimal conditions for performing column chromatography of filamentous phage, leading to the selection of phage peptides that bind specifically to model targets (monoclonal anti-peptide antibodies) with the lowest background obtainable. Specific aims 3 and 4 address the novel DCP subtraction step. Here, optimal chromatographic conditions will be determined for the efficient removal of phage that bind to targets present in both of a pair of samples. In addition, the non-specific background will be further reduced in this step.